ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.1636G>A (p.Gly546Ser)

gnomAD frequency: 0.00003  dbSNP: rs780472818
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000544668 SCV000639107 uncertain significance Oligodontia-cancer predisposition syndrome 2025-01-26 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 546 of the AXIN2 protein (p.Gly546Ser). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with AXIN2-related conditions. ClinVar contains an entry for this variant (Variation ID: 464560). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt AXIN2 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Sema4, Sema4 RCV002257798 SCV002537096 uncertain significance Hereditary cancer-predisposing syndrome 2022-03-17 criteria provided, single submitter curation
Ambry Genetics RCV002257798 SCV002703018 likely benign Hereditary cancer-predisposing syndrome 2023-12-07 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV005231048 SCV005872284 uncertain significance not specified 2025-03-04 criteria provided, single submitter clinical testing

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